This repository hosts data and R code to reproduce the Multi-Species Abundance Model (MSAM) from García-Navas V., López-Poveda G., Bliard L., Christidis L., Ozgul A. (2023). No country for small birds: potential positive association among medium-sized, aggressive species in Australian bird communities. Diveristy and Distributions. https://doi.org/10.1111/ddi.13774
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Title: "Data and code to reproduce the Multi-Species Abundance Model (MSAM) from: No country for small birds, potential positive association among medium-sized, aggressive species in Australian bird communities"
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Author information (for the Multi Species Abundance Model):
Name: Louis Bliard Institution: University of Zurich Email: Louis.bliard@evobio.eu
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Date of data collection (single date, range, approximate date): 1998-2020
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Geographic location of data collection: south-east Queensland
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Information about funding sources that supported the collection of the data: NA
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Licenses/restrictions placed on the data:
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Links to publications that cite or use the data: García-Navas V, López-Povedas G, Bliard L, Chrsitidis L, Ozgul A. 2023. No country for small birds: potential positive association among medium-sized, aggressive species in Australian bird communities. https://doi.org/10.1111/ddi.13774
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Links to other publicly accessible locations of the data: Data associated to "García-Navas V, López-Povedas G, Bliard L, Chrsitidis L, Ozgul A. 2023. No country for small birds: potential positive association among medium-sized, aggressive species in Australian bird communities". Figshare. https://doi.org/10.6084/m9.figshare.20463717.v2
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Links/relationships to ancillary data sets: NA
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Was data derived from another source? yes A. If yes, list source(s): Australian Bird Atlas https://birdata.birdlife.org.au
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Methods for processing the data: All data were processed in R.
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Software-specific information needed to interpret the data: R statistical software, version 4.1.2. JAGS https://mcmc-jags.sourceforge.io/
- File List:
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data_and_output.RData
R data object containing the bird surveys data needed to run the MSAM model, and the output of the model. -
msam_analysis.R
Code containing the JAGS model to run the MSAM analysis, which is used to compute estimated true abundance for species at different sites.
- Relationship between files, if important: The RData file "data_and_output.RData" is needed to run the MSAM analysis with the "msam_analysis.R" file.
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Number of variables: NA
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Number of cases/rows: NA
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Object List:
- f1: vector of length 52 containing the season of first survey for each site.
- f2: vector of length 52 containing the season of last survey for each site.
- Nmat: 4 dimensional array of dimensions 52 (number of sites) * 17 (number of seasons) * 134 (number of species) * 600 (number of saved iterations). This is the output of the MSAM model, and represents the estimated abundance of each species at each site for each season.
- season_vec: vector of length 17 corresponding to each season (starting from season 1998/1999).
- site_vec: vector of length 52 corresponding to each site name.
- species_vec: vector of length 134 corresponding to each species name.
- y: raw occurence data. 4 dimensional array of dimensions 52 (number of sites) * 7 (number of repeated surveys) * 17 (number of seasons) * 134 (number of species).
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Missing data codes: NA
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Specialized formats or other abbreviations used: NA